Merge pull request #88 from miRTop/lpantano-ci

bump python

.github/workflows/python-package-conda.yml

@@ -4,11 +4,13 @@ on:
   push:
     branches:
     - main
+    - master
     - dev
     - release/*
   pull_request:
     branches:
     - main
+    - master
 
 jobs:
   build-linux:
@@ -18,10 +20,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v3
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
@@ -35,8 +37,10 @@ jobs:
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        #flake8 . --count  --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
         conda install pytest
+        python setup.py develop
         pytest

environment.yml

@@ -2,5 +2,6 @@ dependencies:
   - python=3.11
   - bioconda::pysam
   - bioconda::pybedtools
+  - bioconda::samtools=1.21
   - conda-forge::pandas
-  - bioconda::biopython
+  - conda-forge::biopython=1.83

mirtop/mirna/mintplates.py

@@ -509,7 +509,7 @@ def encode_sequence(sequence, prefix):
     """
     length = len(sequence)
     # Encode label
-    if prefix is '':
+    if prefix == '':
         final_result = [(str(length) + '-')]
     else:
         final_result = [prefix + "-" + str(length) + "-"]

scripts/import_gff3.py

@@ -11,7 +11,7 @@ def loadfile(filename,verbose=True):
 
     try:
         if verbose==True:
-            print 'Loading', filename
+            print('Loading', filename)
         # obtaning sample names and number from 3rd line in header
         num_header_lines=0
         with open(filename) as f:
@@ -26,12 +26,12 @@ def loadfile(filename,verbose=True):
                     num_header_lines+=1
         sample_number = len(sample_names)
         if verbose==True:
-            print '--------------------------------------'
-            print sample_number,' samples in the file'
-            print '--------------------------------------'
+            print('--------------------------------------')
+            print(sample_number,' samples in the file')
+            print('--------------------------------------')
             for elem in sample_names:
-                print elem
-            print '--------------------------------------'
+                print(elem)
+            print('--------------------------------------')
 
 
 
@@ -59,11 +59,11 @@ def loadfile(filename,verbose=True):
         num_attr = len(attr_names)                         #number of attributes
         #expression_colindex=attr_names.index ('Expression')  #position of the expression column in the attr column 
         if verbose==True:
-            print num_attr,' attributes in the file '
-            print '--------------------------------------'
+            print(num_attr,' attributes in the file ')
+            print('--------------------------------------')
             for attr in attr_names:
-                print attr
-            print '--------------------------------------'
+                print(attr)
+            print('--------------------------------------')
 
         # joining rows of attributes without the descriptor
         for row in range(atr_data.shape[0]):
@@ -113,7 +113,7 @@ def loadfile(filename,verbose=True):
                     data.at[row.Index,var]=np.nan    
         return data
     except:
-        print 'Error loading the file'
+        print('Error loading the file')
 
 
 """
@@ -137,7 +137,7 @@ def load_check_gff3(filename):
                     data_1=rowfile.split('\t')
                     break
         if coldata_found==False:
-            print 'No COLDATA, bad header'
+            print('No COLDATA, bad header')
             return False
 
         #Number of columns without breaking down attributes column 
@@ -155,33 +155,33 @@ def load_check_gff3(filename):
         for attr in list_attr:    
             if attr not in possible_attr:
                 Error=True
-                print attr,'is not a possible attribute'
+                print(attr,'is not a possible attribute')
                 break  
         if Error:
-            print 'File format error'            
+            print('File format error')
             return False      
         # If not format error, loading content
         try:
             dataframe=loadfile(filename,True)
         except:
-            print 'Error loading file'
+            print('Error loading file')
             return False
-        print 'Checking content'
+        print('Checking content')
         for i in range(dataframe.shape[0]):
             # Labels in type column
             if dataframe.loc[i, 'type'] not in ['ref_miRNA', 'isomiR']:
                 Error = True
-                print'line', i, 'pip install Markdownbad type error'
+                print('line', i, 'pip install Markdownbad type error')
 
             # start<end
             if dataframe.loc[i, 'start'] >= dataframe.loc[i, 'end']:
                 Error = True
-                print 'line', i, 'start >=end error'
+                print('line', i, 'start >=end error')
 
             # Strand + or -
             if dataframe.loc[i, 'strand'] not in ['+', '-']:
                 Error = True
-                print 'line', i, 'bad strand error'
+                print('line', i, 'bad strand error')
             # Variant checking
             possible_variant=['iso_5p','iso_3p','iso_add','iso_snp_seed','iso_snp_central_offset','iso_snp_central',
                   'iso_central_supp','iso_snp_central_supp','iso_snp']
@@ -191,36 +191,36 @@ def load_check_gff3(filename):
             if len(variant_i)==1 and variant_i[0]!='NA':
                 if variant_i[0].split(':')[0] not in possible_variant:
                     Error = True
-                    print 'Variant error', variant_i[0].split(':')[0], 'line', i
+                    print('Variant error', variant_i[0].split(':')[0], 'line', i)
             elif variant_i[0]!='NA':
                 for var in range(len(variant_i)):
                     if variant_i[var].split(':')[0] not in possible_variant:
                         Error = True
-                        print 'Variant error', variant_i[0].split(':')[0], 'line', i
+                        print('Variant error', variant_i[0].split(':')[0], 'line', i)
 
         #Checking expression data
         expression_cols=[col for col in dataframe.columns if 'Expression_' in col]         
         for col in expression_cols:
             for i in range(dataframe.shape[0]):
                 if not dataframe.loc[i,col].isdigit():
-                    print dataframe.loc[i,col].isdigit()
-                    print 'Expression count error line',i
+                    print(dataframe.loc[i,col].isdigit())
+                    print('Expression count error line',i)
                     Error= True
             dataframe[col]=dataframe[col].astype(int) #setting the datatype of counts
             dataframe[col]=dataframe[col].replace(0,np.nan) #Setting 0 reads to NaN
         if 'Filter' in dataframe.columns:         
             for i in range(dataframe.shape[0]):
                 if dataframe.loc[i, 'Filter']!='Pass':
-                    print 'Warning non-pass filter in line',i                   
+                    print('Warning non-pass filter in line',i)
         if Error:
-            print 'File format error'
+            print('File format error')
             return False
 
-        print '--------------------------------------'
-        print dataframe.dtypes
-        print '--------------------------------------'
-        print 'Format ok'
+        print('--------------------------------------')
+        print(dataframe.dtypes)
+        print('--------------------------------------')
+        print('Format ok')
         return dataframe
     except:
-        print 'Error checking the file'
+        print('Error checking the file')
         return False

scripts/prepare.py

@@ -62,7 +62,7 @@ def _download(url, outfn):
     for mir in fa:
         if mir in bed:
             precursor = bed[mir][mir + "_pre"]
-            print precursor
+            print(precursor)
             mir5p = ""
             mir3p = ""
             for mature in bed[mir]:
@@ -82,7 +82,7 @@ def _download(url, outfn):
                 if mature.find("3p") > 0:
                     mir3p = "[%s:%s-%s]" % (mature, start, end)
 
-            print >>OUT, ">%s (X) %s %s" % (mir, mir5p, mir3p)
-            print >>OUTP, ">%s\n%s" % (mir, fa[mir])
+            print(">%s (X) %s %s" % (mir, mir5p, mir3p), file=OUT)
+            print(">%s\n%s" % (mir, fa[mir]),file=OUTP)
 OUT.close()
 OUTP.close()